Deciphering the regulatory network involving the central regulator of chemotaxis and players in the synthesis and detection of c-di-GMP through a combination of in silico, in vitro and in vivo approaches

The project aimed to study the complex regulatory network involving the secondary messenger cyclic di-GMP and its effectors, diguanylate cyclases (DGCs) and the central regulator of chemotaxis CheY. The latter plays a dual role in the aquatic bacterium Shewanella oneidensis, controlling chemotaxis (classical) and biofilm biogenesis (unexpected). The project also aimed to develop deep-learning approaches to better define the players of c-di-GMP (synthesis by DGCs, degradation by phosphodiesterases (PDEs), and detection by effectors) and to reclassify the CheY and CheY-like proteins. It was structured around 3 main tasks: i) Generation of a database grouping DGCs, PDEs and c-di-GMP effectors; ii) Characterization of the interactions of CheY with its DGC and c-di-GMP effector partners; iii) Classification of CheY and CheY-like proteins and definition of a signature specific to CheY proteins presenting, like CheY of S. oneidensis, a dual role in chemotaxis and in another process (biofilm, or other).